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4om8

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Revision as of 07:32, 25 January 2023

Crystal structure of 5-formly-3-hydroxy-2-methylpyridine 4-carboxylic acid (FHMPC) 5-dehydrogenase, an NAD+ dependent dismutase.

Structural highlights

4om8 is a 2 chain structure with sequence from Mesorhizobium japonicum MAFF 303099. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

FHMCD_RHILO Involved in the degradation of pyridoxine (vitamin B(6)). Catalyzes the oxidation of 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate (FHMPC) by NAD(+) to 5-hydroxy-6-methylpyridine-3,4-dicarboxylate (HMPDC) (PubMed:19218190). Can also catalyze the reduction of FHMPC by NADH to 4-pyridoxic acid (PubMed:19218190).^[1]

Publication Abstract from PubMed

5-Formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase (FHMPCDH) from Mesorhizobium loti is the fifth enzyme in degradation pathway I for pyridoxine. The enzyme catalyzes a dismutation reaction: the oxidation of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid (FHMPC) to 3-hydroxy-2-methylpyridine 4,5-dicarboxylic acid with NAD(+) and reduction of FHMPC to 4-pyridoxic acid with NADH. FHMPCDH belongs to the l-3-hydroxyacyl-CoA dehydrogenase (HAD) family. The crystal structure was determined by molecular replacement and refined to a resolution of 1.55A (R-factor of 16.4%, Rfree=19.4%). There were two monomers in the asymmetric unit. The overall structure of the monomer consisted of N- and C-terminal domains connected by a short linker loop. The monomer was similar to members of the HAD family (RMSD=1.9A). The active site was located between the domains and highly conserved to that of human heart l-3-hydroxyacyl-CoA dehydrogenase (HhHAD). His-Glu catalytic dyad, a serine and two asparagine residues of HhHAD were conserved. Ser116, His137 and Glu149 in FHMPCDH are connected by a hydrogen bonding network forming a catalytic triad. The functions of the active site residues in the reaction mechanism are discussed.

Crystal structure of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase, an NAD(+)-dependent dismutase from Mesorhizobium loti.,Mugo AN, Kobayashi J, Mikami B, Yoshikane Y, Yagi T, Ohnishi K Biochem Biophys Res Commun. 2015 Jan 2;456(1):35-40. doi:, 10.1016/j.bbrc.2014.11.028. Epub 2014 Nov 18. PMID:25446130^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Yokochi N, Yoshikane Y, Matsumoto S, Fujisawa M, Ohnishi K, Yagi T. Gene identification and characterization of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase, an NAD+-dependent dismutase. J Biochem. 2009 Apr;145(4):493-503. doi: 10.1093/jb/mvp007. Epub 2009 Jan 17. PMID:19218190 doi:http://dx.doi.org/10.1093/jb/mvp007
↑ Mugo AN, Kobayashi J, Mikami B, Yoshikane Y, Yagi T, Ohnishi K. Crystal structure of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase, an NAD(+)-dependent dismutase from Mesorhizobium loti. Biochem Biophys Res Commun. 2015 Jan 2;456(1):35-40. doi:, 10.1016/j.bbrc.2014.11.028. Epub 2014 Nov 18. PMID:25446130 doi:http://dx.doi.org/10.1016/j.bbrc.2014.11.028

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4om8"

@@ Line 3: / Line 3: @@
 <StructureSection load='4om8' size='340' side='right'caption='[[4om8]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4om8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mesorhizobium_japonicum_(strain_lmg_29417_/_cect_9101_/_maff_303099) Mesorhizobium japonicum (strain lmg 29417 / cect 9101 / maff 303099)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OM8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OM8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4om8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesorhizobium_japonicum_MAFF_303099 Mesorhizobium japonicum MAFF 303099]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OM8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OM8 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Mesorhizobium loti: mlr6793, mlr6793 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266835 Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4om8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4om8 OCA], [https://pdbe.org/4om8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4om8 RCSB], [https://www.ebi.ac.uk/pdbsum/4om8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4om8 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4om8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4om8 OCA], [http://pdbe.org/4om8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4om8 RCSB], [http://www.ebi.ac.uk/pdbsum/4om8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4om8 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/FHMCD_RHILO FHMCD_RHILO] Involved in the degradation of pyridoxine (vitamin B(6)). Catalyzes the oxidation of 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate (FHMPC) by NAD(+) to 5-hydroxy-6-methylpyridine-3,4-dicarboxylate (HMPDC) (PubMed:19218190). Can also catalyze the reduction of FHMPC by NADH to 4-pyridoxic acid (PubMed:19218190).<ref>PMID:19218190</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Kobayashi, J]]
+[[Category: Mesorhizobium japonicum MAFF 303099]]
-[[Category: Mikami, B]]
+[[Category: Kobayashi J]]
-[[Category: Mugo, A N]]
+[[Category: Mikami B]]
-[[Category: Ohnishi, K]]
+[[Category: Mugo AN]]
-[[Category: Yagi, T]]
+[[Category: Ohnishi K]]
-[[Category: Dehydrogenase]]
+[[Category: Yagi T]]
-[[Category: Dismutase]]
-[[Category: Enzyme function initiative]]
-[[Category: Nad-binding]]
-[[Category: Oxidoreductase]]
-[[Category: Rossmann fold]]
-[[Category: Structural genomic]]

4om8

From Proteopedia

Revision as of 07:32, 25 January 2023

Crystal structure of 5-formly-3-hydroxy-2-methylpyridine 4-carboxylic acid (FHMPC) 5-dehydrogenase, an NAD+ dependent dismutase.

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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